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Commit 9ebae55

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lmperrylmperry
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v0.2 rewrite: respect mri_deface exit status, remove logging, support nifti and mgh concurrent output
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‎run‎

Lines changed: 114 additions & 70 deletions
Original file line numberDiff line numberDiff line change
@@ -1,78 +1,122 @@
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#! /bin/bash
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# This script is meant to evoke the algorithm without requiring any input arguments
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#
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LOG_FILE=/flywheel/v0/output/mri-deface.log
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(
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# Define directory names and containers
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FLYWHEEL_BASE=/flywheel/v0
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INPUT_DIR=$FLYWHEEL_BASE/input/anatomical
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OUTPUT_DIR=$FLYWHEEL_BASE/output
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CONFIG_FILE=$FLYWHEEL_BASE/config.json
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CONTAINER='[flywheel/mri-deface]'
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# Define brain and face templates
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brain_template=$FLYWHEEL_BASE/talairach_mixed_with_skull.gca
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face_template=$FLYWHEEL_BASE/face.gca
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# Check if the input directory is not empty
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if [[ "$(ls -A $INPUT_DIR)" ]] ; then
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echo "$CONTAINER Starting..."
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else
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echo "Input directory is empty: $INPUT_DIR"
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exit 1
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fi
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# Run script for flywheel/mri-deface Gear.
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#
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# Authorship: Jennifer Reiter, Michael Perry
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#
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##############################################################################
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# Define directory names and containers
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FLYWHEEL_BASE=/flywheel/v0
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INPUT_DIR=$FLYWHEEL_BASE/input/anatomical
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OUTPUT_DIR=$FLYWHEEL_BASE/output
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CONFIG_FILE=$FLYWHEEL_BASE/config.json
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CONTAINER='[flywheel/mri-deface]'
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##############################################################################
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# Parse configuration options
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# If config.json exists, then we parse config file and cast vals to ENV Vars
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# (Flywheel gear run). Otherwise we parse manifest.json and cast the values to
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# ENV Vars from manifest (Docker run) Note value.default is used to grab the
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# configured defaults.
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if [[ -f $CONFIG_FILE ]]; then
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eval $(jq -r '.config | to_entries[] | "config_\(.key)=\(.value)"' $CONFIG_FILE)
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else
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CONFIG_FILE=$FLYWHEEL_BASE/manifest.json
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eval $(jq -r '.config | to_entries[] | "config_\(.key)=\(.value.default)"' $CONFIG_FILE)
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fi
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##############################################################################
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# Define brain and face templates
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brain_template=$FLYWHEEL_BASE/talairach_mixed_with_skull.gca
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face_template=$FLYWHEEL_BASE/face.gca
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# Find input file in input directory with the extension .nii, .nii.gz, .mgz or .mgh.gz or a .zip dicom file
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input_file=`find $INPUT_DIR -iname '*.nii' -o -iname '*.nii.gz' -o -iname '*.mgz' -o -iname '*.mgh.gz' -o -iname '*.zip'`
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# Check if input file exists
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if [[ -e $input_file ]]
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then
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## Define extension of the input file
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bni=`basename "$input_file"`
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filename="${bni%%.*}"
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inextension="${bni#*.}"
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# If input extension is .zip, then unzip the files (assuming they are DICOM files)
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if [[ $inextension == "zip" ]]
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then
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echo "Unzipping DICOM files"
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unzip $input_file -d $INPUT_DIR
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# Now that the DICOM files are unzipped, need to find one filename to pass to the mri deface software
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input_file=`find $INPUT_DIR -iname '*.dcm' | head -n 1`
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fi
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## Define extension of the output file
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# Get output file extension from config file, if it exists
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if [[ -e $CONFIG_FILE ]]
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then
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echo "Config file is present"
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outextension=`cat $CONFIG_FILE | jq -r '.config.output_extension'`
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echo "The extension read from the config file: $outextension"
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# Otherwise, define output file extension as nifti (.nii.gz)
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else
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outextension=".nii.gz"
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echo "No config file found, so default extension ($outextension) is being used for output"
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fi
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# Define output file to be passed to mri_deface
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output_file=$OUTPUT_DIR/$filename'_deface'$outextension
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/flywheel/v0/mri_deface $input_file $brain_template $face_template $output_file
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else
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echo "No Nifti, DICOM or MGZ inputs were found within input directory $INPUT_DIR"
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exit 1
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##############################################################################
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# Handle INPUT file
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# Find input file In input directory with the extension
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# .nii, .nii.gz, .mgz or .mgh.gz or a .zip DICOM file
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input_file=`find $INPUT_DIR -iname '*.nii' -o -iname '*.nii.gz' -o -iname '*.mgz' -o -iname '*.mgh.gz' -o -iname '*.zip'`
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# Check that input file exists
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if [[ -e $input_file ]]; then
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echo "${CONTAINER} Input file found: ${input_file}"
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# Determine the type of the input file
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if [[ "$input_file" == *.zip ]]; then
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type=".zip"
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elif [[ "$input_file" == *.nii ]]; then
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type=".nii"
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elif [[ "$input_file" == *.nii.gz ]]; then
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type=".nii.gz"
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elif [[ "$input_file" == *.mgz ]]; then
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type=".mgz"
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elif [[ "$input_file" == *.mgz.gz ]]; then
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type=".mgz.gz"
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fi
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# Get a list of the files in the output directory
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outputs=`find $OUTPUT_DIR -type f -name "*"`
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# If outputs exist, then go on...
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if [[ -z $outputs ]]
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then
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echo "No results found in output directory... Exiting"
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exit 1
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else
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chmod -R 777 $OUTPUT_DIR
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echo -e "Wrote: `ls $OUTPUT_DIR`"
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# Get the base filename
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base_filename=`basename "$input_file" $type`
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else
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echo "${CONTAINER} No Nifti, DICOM or MGZ inputs were found within input directory $INPUT_DIR"
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exit 1
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fi
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# If input extension is .zip, then unzip the files (assuming they are DICOM files)
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if [[ "$type" == *.zip ]]; then
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echo "${CONTAINER} Unzipping DICOM files..."
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unzip_dir=$INPUT_DIR/unzipped
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unzip $input_file -d $unzip_dir
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# Now that the DICOM files are unzipped, need to find the full path to the
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# first file to pass mri_deface
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input_file=`find $unzip_dir/* -type f | head -n 1`
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if [[ -e $input_file ]]; then
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echo "$CONTAINER Input file set to: $input_file"
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else
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echo "${CONTAINER} No input file found in: ${input_file}"
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exit 1
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fi
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fi
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##############################################################################
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# Run MRI_DEFACE algorithm
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# Set initial exit status
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mri_deface_exit_status_nifti=0
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mri_deface_exit_status_mgz=0
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# Set base output_file name
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output_file=$OUTPUT_DIR/"$base_filename"'_deface'
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# Check if user wanted NIfTI output
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if [[ $config_output_nifti == 'true' ]]; then
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/flywheel/v0/mri_deface "$input_file" "$brain_template" "$face_template" "$output_file"'.nii.gz'
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mri_deface_exit_status_nifti=$?
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fi
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# Check if user wanted MGH output
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if [[ $config_output_mgh == 'true' ]]; then
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/flywheel/v0/mri_deface "$input_file" "$brain_template" "$face_template" "$output_file"'.mgz'
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mri_deface_exit_status_mgz=$?
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fi
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##############################################################################
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# Handle Exit status
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if [[ $mri_deface_exit_status_nifti == 0 ]] && [[ $mri_deface_exit_status_mgz == 0 ]]; then
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echo -e "${CONTAINER} Success!"
77118
exit 0
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) 2>&1 | tee $LOG_FILE
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else
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echo "${CONTAINER} Something went wrong! mri_deface exited non-zero!"
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exit 1
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fi

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